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Aliases for PCDHGA3 Gene

Aliases for PCDHGA3 Gene

  • Protocadherin Gamma Subfamily A, 3 2 3 5
  • PCDH-GAMMA-A3 3 4

External Ids for PCDHGA3 Gene

Previous GeneCards Identifiers for PCDHGA3 Gene

  • GC05P140540
  • GC05P141302
  • GC05P140702
  • GC05P140747
  • GC05P140781
  • GC05P140699
  • GC05P140810
  • GC05P141035
  • GC05P135868
  • GC05P141101
  • GC05P141139
  • GC05P141179
  • GC05P141210
  • GC05P141249
  • GC05P141297
  • GC05P141375
  • GC05P141444
  • GC05P141518

Summaries for PCDHGA3 Gene

Entrez Gene Summary for PCDHGA3 Gene

  • This gene is a member of the protocadherin gamma gene cluster, one of three related clusters tandemly linked on chromosome five. These gene clusters have an immunoglobulin-like organization, suggesting that a novel mechanism may be involved in their regulation and expression. The gamma gene cluster includes 22 genes divided into 3 subfamilies. Subfamily A contains 12 genes, subfamily B contains 7 genes and 2 pseudogenes, and the more distantly related subfamily C contains 3 genes. The tandem array of 22 large, variable region exons are followed by a constant region, containing 3 exons shared by all genes in the cluster. Each variable region exon encodes the extracellular region, which includes 6 cadherin ectodomains and a transmembrane region. The constant region exons encode the common cytoplasmic region. These neural cadherin-like cell adhesion proteins most likely play a critical role in the establishment and function of specific cell-cell connections in the brain. Alternative splicing has been described for the gamma cluster genes. [provided by RefSeq, Jul 2008]

GeneCards Summary for PCDHGA3 Gene

PCDHGA3 (Protocadherin Gamma Subfamily A, 3) is a Protein Coding gene. GO annotations related to this gene include calcium ion binding. An important paralog of this gene is PCDHGA5.

UniProtKB/Swiss-Prot for PCDHGA3 Gene

  • Potential calcium-dependent cell-adhesion protein. May be involved in the establishment and maintenance of specific neuronal connections in the brain.

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PCDHGA3 Gene

Genomics for PCDHGA3 Gene

Regulatory Elements for PCDHGA3 Gene

Enhancers for PCDHGA3 Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around PCDHGA3 on UCSC Golden Path with GeneCards custom track

Promoters for PCDHGA3 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around PCDHGA3 on UCSC Golden Path with GeneCards custom track

Genomic Location for PCDHGA3 Gene

141,343,829 bp from pter
141,512,979 bp from pter
169,151 bases
Plus strand

Genomic View for PCDHGA3 Gene

Genes around PCDHGA3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PCDHGA3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PCDHGA3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PCDHGA3 Gene

Proteins for PCDHGA3 Gene

  • Protein details for PCDHGA3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protocadherin gamma-A3
    Protein Accession:
    Secondary Accessions:
    • Q9Y5D4

    Protein attributes for PCDHGA3 Gene

    932 amino acids
    Molecular mass:
    100971 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for PCDHGA3 Gene


neXtProt entry for PCDHGA3 Gene

Proteomics data for PCDHGA3 Gene at MOPED

Post-translational modifications for PCDHGA3 Gene

  • Glycosylation at Asn 265, Asn 419, Asn 545, and Asn 685
  • Modification sites at PhosphoSitePlus

Other Protein References for PCDHGA3 Gene

No data available for DME Specific Peptides for PCDHGA3 Gene

Domains & Families for PCDHGA3 Gene

Gene Families for PCDHGA3 Gene

Protein Domains for PCDHGA3 Gene

Suggested Antigen Peptide Sequences for PCDHGA3 Gene

Graphical View of Domain Structure for InterPro Entry



  • Contains 6 cadherin domains.
  • Contains 6 cadherin domains.
genes like me logo Genes that share domains with PCDHGA3: view

Function for PCDHGA3 Gene

Molecular function for PCDHGA3 Gene

UniProtKB/Swiss-Prot Function:
Potential calcium-dependent cell-adhesion protein. May be involved in the establishment and maintenance of specific neuronal connections in the brain.

Phenotypes for PCDHGA3 Gene

GenomeRNAi human phenotypes for PCDHGA3:
genes like me logo Genes that share phenotypes with PCDHGA3: view

Animal Model Products

CRISPR Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for PCDHGA3 Gene

Localization for PCDHGA3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PCDHGA3 Gene

Cell membrane; Single-pass type I membrane protein.

Subcellular locations from

Jensen Localization Image for PCDHGA3 Gene COMPARTMENTS Subcellular localization image for PCDHGA3 gene
Compartment Confidence
plasma membrane 3
endosome 1
lysosome 1
vacuole 1

No data available for Gene Ontology (GO) - Cellular Components for PCDHGA3 Gene

Pathways & Interactions for PCDHGA3 Gene

SuperPathways for PCDHGA3 Gene

No Data Available

Interacting Proteins for PCDHGA3 Gene

Gene Ontology (GO) - Biological Process for PCDHGA3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007155 cell adhesion IEA --
genes like me logo Genes that share ontologies with PCDHGA3: view

No data available for Pathways by source and SIGNOR curated interactions for PCDHGA3 Gene

Drugs & Compounds for PCDHGA3 Gene

(1) Drugs for PCDHGA3 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
calcium Nutra 0
genes like me logo Genes that share compounds with PCDHGA3: view

Transcripts for PCDHGA3 Gene

Alternative Splicing Database (ASD) splice patterns (SP) for PCDHGA3 Gene

No ASD Table

Relevant External Links for PCDHGA3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PCDHGA3 Gene

mRNA expression in normal human tissues for PCDHGA3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for PCDHGA3 Gene

This gene is overexpressed in Plasma (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for PCDHGA3 Gene

genes like me logo Genes that share expression patterns with PCDHGA3: view

Protein tissue co-expression partners for PCDHGA3 Gene

- Elite partner

Primer Products

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for PCDHGA3 Gene

Orthologs for PCDHGA3 Gene

This gene was present in the common ancestor of chordates.

Orthologs for PCDHGA3 Gene

Organism Taxonomy Gene Similarity Type Details
(Bos Taurus)
Mammalia PCDHGB1 35
  • 85.63 (n)
  • 86.71 (a)
  • 86 (a)
(Canis familiaris)
Mammalia PCDHGA3 35
  • 84.57 (n)
  • 83.04 (a)
(Mus musculus)
Mammalia Pcdhga3 35
  • 83.3 (n)
  • 85.84 (a)
Pcdhga3 16
(Pan troglodytes)
Mammalia PCDHGA3 35
  • 99.32 (n)
  • 99.25 (a)
(Rattus norvegicus)
Mammalia Pcdhga3 35
  • 84.06 (n)
  • 86.53 (a)
(Monodelphis domestica)
Mammalia -- 36
  • 65 (a)
-- 36
  • 66 (a)
-- 36
  • 65 (a)
(Ornithorhynchus anatinus)
Mammalia -- 36
  • 67 (a)
-- 36
  • 66 (a)
-- 36
  • 65 (a)
-- 36
  • 68 (a)
-- 36
  • 59 (a)
-- 36
  • 66 (a)
(Gallus gallus)
Aves -- 36
  • 50 (a)
-- 36
  • 50 (a)
(Anolis carolinensis)
Reptilia -- 36
  • 53 (a)
-- 36
  • 53 (a)
-- 36
  • 51 (a)
-- 36
  • 52 (a)
-- 36
  • 54 (a)
-- 36
  • 54 (a)
-- 36
  • 50 (a)
-- 36
  • 54 (a)
Species with no ortholog for PCDHGA3:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for PCDHGA3 Gene

Gene Tree for PCDHGA3 (if available)
Gene Tree for PCDHGA3 (if available)

Paralogs for PCDHGA3 Gene

genes like me logo Genes that share paralogs with PCDHGA3: view

Variants for PCDHGA3 Gene

Sequence variations from dbSNP and Humsavar for PCDHGA3 Gene

SNP ID Clin Chr 05 pos Sequence Context AA Info Type
VAR_055588 -
VAR_055589 -
VAR_059190 -

Structural Variations from Database of Genomic Variants (DGV) for PCDHGA3 Gene

Variant ID Type Subtype PubMed ID
dgv1857e1 CNV Complex 17122850
dgv6351n71 CNV Loss 21882294
dgv6352n71 CNV Loss 21882294
dgv6353n71 CNV Loss 21882294
nsv882987 CNV Gain 21882294
nsv882990 CNV Loss 21882294
nsv823279 CNV Gain 20364138
nsv823280 CNV Loss 20364138
nsv519627 CNV Loss 19592680
esv267823 CNV Insertion 20981092
nsv518799 CNV Loss 19592680
nsv327707 CNV Loss 16902084
esv2730847 CNV Deletion 23290073
nsv462470 CNV Loss 19166990
esv25744 CNV Gain 19812545

Variation tolerance for PCDHGA3 Gene

Residual Variation Intolerance Score: 19.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.75; 78.86% of all genes are more intolerant (likely to be disease-causing)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Relevant External Links for PCDHGA3 Gene

Disorders for PCDHGA3 Gene

Relevant External Links for PCDHGA3

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:

No disorders were found for PCDHGA3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for PCDHGA3 Gene

Publications for PCDHGA3 Gene

  1. A striking organization of a large family of human neural cadherin- like cell adhesion genes. (PMID: 10380929) Wu Q. … Maniatis T. (Cell 1999) 2 3 4 67
  2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose J.E. … Uhl G.R. (Mol. Med. 2010) 3
  3. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PMID: 12477932) Strausberg R.L. … Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002) 3
  4. Comparative DNA sequence analysis of mouse and human protocadherin gene clusters. (PMID: 11230163) Wu Q. … Maniatis T. (Genome Res. 2001) 3
  5. Large exons encoding multiple ectodomains are a characteristic feature of protocadherin genes. (PMID: 10716726) Wu Q. … Maniatis T. (Proc. Natl. Acad. Sci. U.S.A. 2000) 3

Products for PCDHGA3 Gene

Sources for PCDHGA3 Gene